Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	D	A	P	S	T	T	P	H	D	A	V	F	K	Q	F	L	M	H	A	E	T	A	R	D	F	L	E	I	H	L	P	V	E	L	R	E	L	C	D	L	N	T	L	H	L	E	S	G	S	F	I	E	E	S	L	K	G	H	S
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?																																							?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		T	D	V	L	Y	S	V	Q	M	Q	G	N	P	G	Y	L	H	V	V	I	E	H	Q	S	K	P	D	K	K	M	A	F	R	M	M	R	Y	S	I	A	A	M	H	R	H	L	E	A	D	H	D	K	L	P	L	V	V	P	I	L
Secondary structure
SS confidence
Disorder																																																?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		F	Y	Q	G	E	A	T	P	Y	P	L	S	M	C	W	F	D	M	F	Y	S	P	E	L	A	R	R	V	Y	N	S	P	F	P	L	V	D	I	T	I	T	P	D	D	E	I	M	Q	H	R	R	I	A	I	L	E	L	L	Q	K
Secondary structure
SS confidence
Disorder							?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		H	I	R	Q	R	D	L	M	L	L	L	E	Q	L	V	T	L	I	D	E	G	Y	T	S	G	S	Q	L	V	A	M	Q	N	Y	M	L	Q	R	G	H	T	E	Q	A	D	L	F	Y	G	V	L	R	D	R	E	T	G	G	E	S
Secondary structure
SS confidence
Disorder																																										?	?	?											?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		M	M	T	L	A	Q	W	F	E	E	K	G	I	E	K	G	I	Q	Q	G	R	Q	E	V	S	Q	E	F	A	Q	R	L	L	S	K	G	M	S	R	E	D	V	A	E	M	A	N	L	P	L	A	E	I	D	K	V	I	N	L	I
Secondary structure
SS confidence
Disorder																																				?	?	?																					?	?	?
Disorder confidence
Sequence
Secondary structure
SS confidence
Disorder
Disorder confidence

Confidence Key
High(9)											Low (0)

?	Disordered
	Alpha helix
	Beta strand

Domain analysis

Hover over an aligned region to see model and summary info

Please note, only up to the top 20 hits are modelled to reduce computer load

Rank Aligned region

PDB 2x48 chain B Region: 266 - 297 Aligned: 32 Modelled: 32 Confidence: 89.8% Identity: 13% PDB header:viral protein Chain: B: PDB Molecule:cag38821; PDBTitle: orf 55 from sulfolobus islandicus rudivirus 1 Phyre2 PDB 2gm4 chain B Region: 225 - 298 Aligned: 74 Modelled: 74 Confidence: 87.0% Identity: 12% PDB header:recombination, dna Chain: B: PDB Molecule:transposon gamma-delta resolvase; PDBTitle: an activated, tetrameric gamma-delta resolvase: hin chimaera bound to2 cleaved dna Phyre2 PDB 1a9x chain A domain 1 Region: 203 - 298 Aligned: 96 Modelled: 96 Confidence: 83.9% Identity: 17% Fold: Carbamoyl phosphate synthetase, large subunit connection domain Superfamily: Carbamoyl phosphate synthetase, large subunit connection domain Family: Carbamoyl phosphate synthetase, large subunit connection domain Phyre2 PDB 1p4w chain A Region: 264 - 300 Aligned: 37 Modelled: 37 Confidence: 82.4% Identity: 16% Fold: DNA/RNA-binding 3-helical bundle Superfamily: C-terminal effector domain of the bipartite response regulators Family: GerE-like (LuxR/UhpA family of transcriptional regulators) Phyre2 PDB 1s6l chain A domain 1 Region: 269 - 300 Aligned: 32 Modelled: 32 Confidence: 81.2% Identity: 28% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: MerB N-terminal domain-like Phyre2 PDB 1vz0 chain A domain 1 Region: 264 - 299 Aligned: 36 Modelled: 36 Confidence: 79.6% Identity: 22% Fold: DNA/RNA-binding 3-helical bundle Superfamily: KorB DNA-binding domain-like Family: KorB DNA-binding domain-like Phyre2 PDB 1x3u chain A Region: 264 - 300 Aligned: 37 Modelled: 37 Confidence: 79.4% Identity: 5% PDB header:transcription Chain: A: PDB Molecule:transcriptional regulatory protein fixj; PDBTitle: solution structure of the c-terminal transcriptional2 activator domain of fixj from sinorhizobium melilot Phyre2 PDB 1h0m chain D Region: 264 - 300 Aligned: 37 Modelled: 37 Confidence: 78.8% Identity: 11% PDB header:transcription/dna Chain: D: PDB Molecule:transcriptional activator protein trar; PDBTitle: three-dimensional structure of the quorum sensing protein2 trar bound to its autoinducer and to its target dna Phyre2 PDB 1r71 chain B Region: 264 - 299 Aligned: 36 Modelled: 36 Confidence: 78.7% Identity: 28% PDB header:transcription/dna Chain: B: PDB Molecule:transcriptional repressor protein korb; PDBTitle: crystal structure of the dna binding domain of korb in2 complex with the operator dna Phyre2 PDB 1fse chain A Region: 264 - 300 Aligned: 37 Modelled: 37 Confidence: 78.5% Identity: 11% Fold: DNA/RNA-binding 3-helical bundle Superfamily: C-terminal effector domain of the bipartite response regulators Family: GerE-like (LuxR/UhpA family of transcriptional regulators) Phyre2 PDB 2jpc chain A Region: 265 - 300 Aligned: 36 Modelled: 36 Confidence: 77.9% Identity: 8% PDB header:dna binding protein Chain: A: PDB Molecule:ssrb; PDBTitle: ssrb dna binding protein Phyre2 PDB 1a04 chain A domain 1 Region: 264 - 300 Aligned: 37 Modelled: 37 Confidence: 77.7% Identity: 8% Fold: DNA/RNA-binding 3-helical bundle Superfamily: C-terminal effector domain of the bipartite response regulators Family: GerE-like (LuxR/UhpA family of transcriptional regulators) Phyre2 PDB 2krf chain B Region: 264 - 300 Aligned: 37 Modelled: 37 Confidence: 77.4% Identity: 16% PDB header:transcription Chain: B: PDB Molecule:transcriptional regulatory protein coma; PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a Phyre2 PDB 1q1h chain A Region: 266 - 298 Aligned: 33 Modelled: 33 Confidence: 77.0% Identity: 30% PDB header:transcription Chain: A: PDB Molecule:transcription factor e; PDBTitle: an extended winged helix domain in general transcription2 factor e/iie alpha Phyre2 PDB 1q1h chain A Region: 266 - 298 Aligned: 33 Modelled: 33 Confidence: 77.0% Identity: 30% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Transcription factor E/IIe-alpha, N-terminal domain Phyre2 PDB 1r71 chain A Region: 264 - 299 Aligned: 36 Modelled: 36 Confidence: 75.9% Identity: 28% Fold: DNA/RNA-binding 3-helical bundle Superfamily: KorB DNA-binding domain-like Family: KorB DNA-binding domain-like Phyre2 PDB 1yio chain A domain 1 Region: 264 - 300 Aligned: 37 Modelled: 37 Confidence: 75.6% Identity: 11% Fold: DNA/RNA-binding 3-helical bundle Superfamily: C-terminal effector domain of the bipartite response regulators Family: GerE-like (LuxR/UhpA family of transcriptional regulators) Phyre2 PDB 2rnj chain A Region: 265 - 300 Aligned: 36 Modelled: 36 Confidence: 75.5% Identity: 17% PDB header:transcription Chain: A: PDB Molecule:response regulator protein vrar; PDBTitle: nmr structure of the s. aureus vrar dna binding domain Phyre2 PDB 1zlj chain E Region: 264 - 300 Aligned: 37 Modelled: 37 Confidence: 75.2% Identity: 16% PDB header:transcription Chain: E: PDB Molecule:dormancy survival regulator; PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain Phyre2 PDB 2q0o chain A Region: 264 - 300 Aligned: 37 Modelled: 37 Confidence: 75.1% Identity: 11% PDB header:transcription Chain: A: PDB Molecule:probable transcriptional activator protein trar; PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing Phyre2 1 c2x48B_ 2 c2gm4B_ 3 d1a9xa1 4 d1p4wa_ 5 d1s6la1 6 d1vz0a1 7 c1x3uA_ 8 c1h0mD_ 9 c1r71B_ 10 d1fsea_ 11 c2jpcA_ 12 d1a04a1 13 c2krfB_ 14 c1q1hA_ 15 d1q1ha_ 16 d1r71a_ 17 d1yioa1 18 c2rnjA_ 19 c1zljE_ 20 c2q0oA_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156

Detailed template information

# Template Alignment Coverage 3D Model Confidence % i.d. Template Information

1 c2x48B_ 89.8 13 PDB header:viral protein Chain: B: PDB Molecule:cag38821; PDBTitle: orf 55 from sulfolobus islandicus rudivirus 1 2 c2gm4B_ 87.0 12 PDB header:recombination, dna Chain: B: PDB Molecule:transposon gamma-delta resolvase; PDBTitle: an activated, tetrameric gamma-delta resolvase: hin chimaera bound to2 cleaved dna 3 d1a9xa1 83.9 17 Fold:Carbamoyl phosphate synthetase, large subunit connection domain Superfamily:Carbamoyl phosphate synthetase, large subunit connection domain Family:Carbamoyl phosphate synthetase, large subunit connection domain 4 d1p4wa_ 82.4 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators) 5 d1s6la1 81.2 28 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MerB N-terminal domain-like 6 d1vz0a1 79.6 22 Fold:DNA/RNA-binding 3-helical bundle Superfamily:KorB DNA-binding domain-like Family:KorB DNA-binding domain-like 7 c1x3uA_ 79.4 5 PDB header:transcription Chain: A: PDB Molecule:transcriptional regulatory protein fixj; PDBTitle: solution structure of the c-terminal transcriptional2 activator domain of fixj from sinorhizobium melilot 8 c1h0mD_ 78.8 11 PDB header:transcription/dna Chain: D: PDB Molecule:transcriptional activator protein trar; PDBTitle: three-dimensional structure of the quorum sensing protein2 trar bound to its autoinducer and to its target dna 9 c1r71B_ 78.7 28 PDB header:transcription/dna Chain: B: PDB Molecule:transcriptional repressor protein korb; PDBTitle: crystal structure of the dna binding domain of korb in2 complex with the operator dna 10 d1fsea_ 78.5 11 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators) 11 c2jpcA_ 77.9 8 PDB header:dna binding protein Chain: A: PDB Molecule:ssrb; PDBTitle: ssrb dna binding protein 12 d1a04a1 77.7 8 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators) 13 c2krfB_ 77.4 16 PDB header:transcription Chain: B: PDB Molecule:transcriptional regulatory protein coma; PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a 14 c1q1hA_ 77.0 30 PDB header:transcription Chain: A: PDB Molecule:transcription factor e; PDBTitle: an extended winged helix domain in general transcription2 factor e/iie alpha 15 d1q1ha_ 77.0 30 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Transcription factor E/IIe-alpha, N-terminal domain 16 d1r71a_ 75.9 28 Fold:DNA/RNA-binding 3-helical bundle Superfamily:KorB DNA-binding domain-like Family:KorB DNA-binding domain-like 17 d1yioa1 75.6 11 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators) 18 c2rnjA_ 75.5 17 PDB header:transcription Chain: A: PDB Molecule:response regulator protein vrar; PDBTitle: nmr structure of the s. aureus vrar dna binding domain 19 c1zljE_ 75.2 16 PDB header:transcription Chain: E: PDB Molecule:dormancy survival regulator; PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain 20 c2q0oA_ 75.1 11 PDB header:transcription Chain: A: PDB Molecule:probable transcriptional activator protein trar; PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing 21 c1l0oC_ not modelled 72.2 5 PDB header:protein binding Chain: C: PDB Molecule:sigma factor; PDBTitle: crystal structure of the bacillus stearothermophilus anti-2 sigma factor spoiiab with the sporulation sigma factor3 sigmaf 22 d1l0oc_ not modelled 72.2 5 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 23 c3sztB_ not modelled 71.3 5 PDB header:transcription Chain: B: PDB Molecule:quorum-sensing control repressor; PDBTitle: quorum sensing control repressor, qscr, bound to n-3-oxo-dodecanoyl-l-2 homoserine lactone 24 c3qp5C_ not modelled 69.3 8 PDB header:transcription Chain: C: PDB Molecule:cvir transcriptional regulator; PDBTitle: crystal structure of cvir bound to antagonist chlorolactone (cl) 25 d1l3la1 not modelled 68.1 11 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators) 26 c3cloC_ not modelled 67.8 16 PDB header:transcription regulator Chain: C: PDB Molecule:transcriptional regulator; PDBTitle: crystal structure of putative transcriptional regulator containing a2 luxr dna binding domain (np_811094.1) from bacteroides3 thetaiotaomicron vpi-5482 at 2.04 a resolution 27 d1rp3a1 not modelled 59.5 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma3 domain 28 c1u78A_ not modelled 58.9 6 PDB header:dna binding protein/dna Chain: A: PDB Molecule:transposable element tc3 transposase; PDBTitle: structure of the bipartite dna-binding domain of tc32 transposase bound to transposon dna 29 c3trbA_ not modelled 57.7 16 PDB header:dna binding protein Chain: A: PDB Molecule:virulence-associated protein i; PDBTitle: structure of an addiction module antidote protein of a higa (higa)2 family from coxiella burnetii 30 d1ku2a1 not modelled 57.6 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma3 domain 31 c3c3wB_ not modelled 57.5 16 PDB header:transcription Chain: B: PDB Molecule:two component transcriptional regulatory protein devr; PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic response2 regulator dosr 32 d1ttya_ not modelled 55.5 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 33 c3t76A_ not modelled 54.9 9 PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator vanug; PDBTitle: crystal structure of transcriptional regulator vanug, form ii 34 d2a6ca1 not modelled 53.3 13 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:NE1354 35 d1ku3a_ not modelled 52.7 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 36 c3b7hA_ not modelled 51.9 15 PDB header:structural protein Chain: A: PDB Molecule:prophage lp1 protein 11; PDBTitle: crystal structure of the prophage lp1 protein 11 37 c2r0qF_ not modelled 51.3 13 PDB header:recombination/dna Chain: F: PDB Molecule:putative transposon tn552 dna-invertase bin3; PDBTitle: crystal structure of a serine recombinase- dna regulatory2 complex 38 c2o8xA_ not modelled 49.9 19 PDB header:transcription Chain: A: PDB Molecule:probable rna polymerase sigma-c factor; PDBTitle: crystal structure of the "-35 element" promoter recognition domain of2 mycobacterium tuberculosis sigc 39 c1vz0B_ not modelled 49.7 22 PDB header:nuclear protein Chain: B: PDB Molecule:chromosome partitioning protein parb; PDBTitle: chromosome segregation protein spo0j from thermus2 thermophilus 40 d1uxca_ not modelled 48.9 27 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 41 c1m6vE_ not modelled 48.8 31 PDB header:ligase Chain: E: PDB Molecule:carbamoyl phosphate synthetase large chain; PDBTitle: crystal structure of the g359f (small subunit) point mutant of2 carbamoyl phosphate synthetase 42 d1trra_ not modelled 48.1 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:Trp repressor, TrpR 43 d1ku7a_ not modelled 47.9 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 44 d1jhga_ not modelled 47.9 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:Trp repressor, TrpR 45 d1ic8a2 not modelled 46.6 15 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:POU-specific domain 46 d1q08a_ not modelled 46.2 17 Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:DNA-binding N-terminal domain of transcription activators 47 d1efaa1 not modelled 45.1 33 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 48 d2p7vb1 not modelled 44.4 11 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 49 d1lcda_ not modelled 44.2 33 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 50 d2hsga1 not modelled 43.5 30 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 51 c3fymA_ not modelled 42.2 12 PDB header:dna binding protein Chain: A: PDB Molecule:putative uncharacterized protein; PDBTitle: the 1a structure of ymfm, a putative dna-binding membrane2 protein from staphylococcus aureus 52 d1r8ea1 not modelled 41.9 14 Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:DNA-binding N-terminal domain of transcription activators 53 d1s7oa_ not modelled 40.7 8 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:YlxM/p13-like 54 d1r69a_ not modelled 40.0 12 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 55 d1z6ra1 not modelled 39.8 26 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ROK associated domain 56 c2k9lA_ not modelled 39.5 28 PDB header:transcription Chain: A: PDB Molecule:rna polymerase sigma factor rpon; PDBTitle: structure of the core binding domain of sigma54 57 d1y9qa1 not modelled 39.0 15 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Probable transcriptional regulator VC1968, N-terminal domain 58 d1smyf2 not modelled 38.8 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 59 d1b0na2 not modelled 38.8 24 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like 60 c3klnC_ not modelled 38.4 14 PDB header:transcription Chain: C: PDB Molecule:transcriptional regulator, luxr family; PDBTitle: vibrio cholerae vpst 61 d1uxda_ not modelled 38.0 27 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 62 c2wusR_ not modelled 37.4 9 PDB header:structural protein Chain: R: PDB Molecule:putative uncharacterized protein; PDBTitle: bacterial actin mreb assembles in complex with cell shape2 protein rodz 63 d1ijwc_ not modelled 37.2 27 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain 64 c3mzyA_ not modelled 36.8 15 PDB header:rna binding protein Chain: A: PDB Molecule:rna polymerase sigma-h factor; PDBTitle: the crystal structure of the rna polymerase sigma-h factor from2 fusobacterium nucleatum to 2.5a 65 d2bjca1 not modelled 36.5 38 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 66 c3d6zA_ not modelled 36.2 15 PDB header:transcription regulator/dna Chain: A: PDB Molecule:multidrug-efflux transporter 1 regulator; PDBTitle: crystal structure of r275e mutant of bmrr bound to dna and rhodamine 67 c1rnlA_ not modelled 36.2 8 PDB header:signal transduction protein Chain: A: PDB Molecule:nitrate/nitrite response regulator protein narl; PDBTitle: the nitrate/nitrite response regulator protein narl from narl 68 c3t72o_ not modelled 35.9 13 PDB header:transcription/dna Chain: O: PDB Molecule:pho box dna (strand 1); PDBTitle: phob(e)-sigma70(4)-(rnap-betha-flap-tip-helix)-dna transcription2 activation sub-complex 69 d1adra_ not modelled 35.6 9 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 70 c3frwF_ not modelled 35.4 19 PDB header:structural genomics, unknown function Chain: F: PDB Molecule:putative trp repressor protein; PDBTitle: crystal structure of putative trpr protein from ruminococcus obeum 71 d1hcra_ not modelled 35.1 27 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain 72 c3omtA_ not modelled 34.8 16 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: putative antitoxin component, chu_2935 protein, from xre family from2 prevotella buccae. 73 d1or7a1 not modelled 34.4 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 74 d1xsva_ not modelled 34.4 11 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:YlxM/p13-like 75 c3clcC_ not modelled 33.4 30 PDB header:transcription regulator/dna Chain: C: PDB Molecule:regulatory protein; PDBTitle: crystal structure of the restriction-modification controller protein2 c.esp1396i tetramer in complex with its natural 35 base-pair operator 76 c2ebyA_ not modelled 33.3 19 PDB header:transcription Chain: A: PDB Molecule:putative hth-type transcriptional regulator ybaq; PDBTitle: crystal structure of a hypothetical protein from e. coli 77 c2q1zA_ not modelled 33.1 22 PDB header:transcription Chain: A: PDB Molecule:rpoe, ecf sige; PDBTitle: crystal structure of rhodobacter sphaeroides sige in complex with the2 anti-sigma chrr 78 d1d5ya1 not modelled 32.9 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:AraC type transcriptional activator 79 c2jvlA_ not modelled 32.9 9 PDB header:transcription Chain: A: PDB Molecule:trmbf1; PDBTitle: nmr structure of the c-terminal domain of mbf1 of trichoderma reesei 80 d1dpua_ not modelled 32.7 10 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:C-terminal domain of RPA32 81 c1dpuA_ not modelled 32.7 10 PDB header:dna binding protein Chain: A: PDB Molecule:replication protein a (rpa32) c-terminal domain; PDBTitle: solution structure of the c-terminal domain of human rpa322 complexed with ung2(73-88) 82 d1vola2 not modelled 32.5 13 Fold:Cyclin-like Superfamily:Cyclin-like Family:Transcription factor IIB (TFIIB), core domain 83 d2iv2x2 not modelled 32.2 19 Fold:Formate dehydrogenase/DMSO reductase, domains 1-3 Superfamily:Formate dehydrogenase/DMSO reductase, domains 1-3 Family:Formate dehydrogenase/DMSO reductase, domains 1-3 84 d1bl0a2 not modelled 31.6 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:AraC type transcriptional activator 85 c3hugA_ not modelled 31.5 14 PDB header:transcription/membrane protein Chain: A: PDB Molecule:rna polymerase sigma factor; PDBTitle: crystal structure of mycobacterium tuberculosis anti-sigma factor rsla2 in complex with -35 promoter binding domain of sigl 86 d2icta1 not modelled 31.4 11 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like 87 c3hh0C_ not modelled 30.8 11 PDB header:transcription regulator Chain: C: PDB Molecule:transcriptional regulator, merr family; PDBTitle: crystal strucure of a transcriptional regulator, merr family2 from bacillus cereus 88 d1h0ha2 not modelled 30.6 15 Fold:Formate dehydrogenase/DMSO reductase, domains 1-3 Superfamily:Formate dehydrogenase/DMSO reductase, domains 1-3 Family:Formate dehydrogenase/DMSO reductase, domains 1-3 89 d1hq1a_ not modelled 30.3 6 Fold:Signal peptide-binding domain Superfamily:Signal peptide-binding domain Family:Signal peptide-binding domain 90 c1h0hA_ not modelled 29.9 15 PDB header:dehydrogenase Chain: A: PDB Molecule:formate dehydrogenase (large subunit); PDBTitle: tungsten containing formate dehydrogenase from2 desulfovibrio gigas 91 d1dula_ not modelled 29.6 6 Fold:Signal peptide-binding domain Superfamily:Signal peptide-binding domain Family:Signal peptide-binding domain 92 d1pdnc_ not modelled 29.4 8 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 93 c1or7A_ not modelled 29.3 19 PDB header:transcription Chain: A: PDB Molecule:rna polymerase sigma-e factor; PDBTitle: crystal structure of escherichia coli sigmae with the cytoplasmic2 domain of its anti-sigma rsea 94 d2cyya1 not modelled 29.2 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 95 d1z05a1 not modelled 29.1 26 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ROK associated domain 96 d2o38a1 not modelled 29.0 8 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:NE1354 97 c2o38A_ not modelled 29.0 8 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein; PDBTitle: putative xre family transcriptional regulator 98 c2l8nA_ not modelled 28.4 24 PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional repressor cytr; PDBTitle: nmr structure of the cytidine repressor dna binding domain in presence2 of operator half-site dna 99 c2iv2X_ not modelled 28.4 19 PDB header:oxidoreductase Chain: X: PDB Molecule:formate dehydrogenase h; PDBTitle: reinterpretation of reduced form of formate dehydrogenase h2 from e. coli 100 c3op9A_ not modelled 28.1 12 PDB header:transcription regulator Chain: A: PDB Molecule:pli0006 protein; PDBTitle: crystal structure of transcriptional regulator from listeria innocua 101 d1y7ya1 not modelled 28.1 24 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like 102 d2croa_ not modelled 28.1 15 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 103 d1qpza1 not modelled 27.7 38 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 104 d1j5ya1 not modelled 27.6 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Biotin repressor-like 105 d1kqfa2 not modelled 27.4 19 Fold:Formate dehydrogenase/DMSO reductase, domains 1-3 Superfamily:Formate dehydrogenase/DMSO reductase, domains 1-3 Family:Formate dehydrogenase/DMSO reductase, domains 1-3 106 c3f52A_ not modelled 27.3 12 PDB header:transcription activator Chain: A: PDB Molecule:clp gene regulator (clgr); PDBTitle: crystal structure of the clp gene regulator clgr from c. glutamicum 107 d1utxa_ not modelled 27.2 13 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like 108 c2e7zA_ not modelled 27.1 23 PDB header:lyase Chain: A: PDB Molecule:acetylene hydratase ahy; PDBTitle: acetylene hydratase from pelobacter acetylenicus 109 c3dfgA_ not modelled 27.0 14 PDB header:recombination Chain: A: PDB Molecule:regulatory protein recx; PDBTitle: crystal structure of recx: a potent inhibitor protein of2 reca from xanthomonas campestris 110 d2et1a1 not modelled 26.9 0 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein 111 c2v45A_ not modelled 26.6 23 PDB header:oxidoreductase Chain: A: PDB Molecule:periplasmic nitrate reductase; PDBTitle: a new catalytic mechanism of periplasmic nitrate reductase2 from desulfovibrio desulfuricans atcc 27774 from3 crystallographic and epr data and based on detailed4 analysis of the sixth ligand 112 d1sq8a_ not modelled 26.6 15 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 113 c2npuA_ not modelled 26.6 22 PDB header:transferase Chain: A: PDB Molecule:fkbp12-rapamycin complex-associated protein; PDBTitle: the solution structure of the rapamycin-binding domain of2 mtor (frb) 114 c2kpjA_ not modelled 26.5 5 PDB header:transcription regulator Chain: A: PDB Molecule:sos-response transcriptional repressor, lexa; PDBTitle: solution structure of protein sos-response transcriptional2 repressor, lexa from eubacterium rectale. northeast3 structural genomics consortium target err9a 115 d2cg4a1 not modelled 26.0 9 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 116 c2vpyE_ not modelled 25.9 19 PDB header:oxidoreductase Chain: E: PDB Molecule:thiosulfate reductase; PDBTitle: polysulfide reductase with bound quinone inhibitor,2 pentachlorophenol (pcp) 117 c2lcvA_ not modelled 25.7 24 PDB header:transcription regulator Chain: A: PDB Molecule:hth-type transcriptional repressor cytr; PDBTitle: structure of the cytidine repressor dna-binding domain; an alternate2 calculation 118 c3cecA_ not modelled 25.6 26 PDB header:transcription Chain: A: PDB Molecule:putative antidote protein of plasmid maintenance system; PDBTitle: crystal structure of a putative antidote protein of plasmid2 maintenance system (npun_f2943) from nostoc punctiforme pcc 73102 at3 1.60 a resolution 119 d2r1jl1 not modelled 25.5 9 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 120 d1k78a1 not modelled 25.5 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain

Binding site prediction

Due to computational demand, binding site predictions are not run for batch jobs

If you want to predict binding sites, please manually submit your model of choice to 3DLigandSite

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Phyre is for academic use only

Please cite: Protein structure prediction on the web: a case study using the Phyre server
Kelley LA and Sternberg MJE. Nature Protocols 4, 363 - 371 (2009) [pdf] [Import into BibTeX]
If you use the binding site predictions from 3DLigandSite, please also cite:
3DLigandSite: predicting ligand-binding sites using similar structures.
Wass MN, Kelley LA and Sternberg MJ Nucleic Acids Research 38, W469-73 (2010) [PubMed]
© Structural Bioinformatics Group Imperial College London Lawrence Kelley, Benjamin Jefferys Disclaimer Terms and Conditions	Component software Template detection: HHpred 1.51 Secondary structure prediction: Psi-pred 2.5 Disorder prediction: Disopred 2.4 Transmembrane prediction: Memsat_SVM Multi-template modelling and ab initio: Poing 1.0